Sun; Routes where it is encountered naturally: Eastern Hoenn water routes (after Groudon is awakened, before it is battled), Routes 114, 115, 116, and 118 when Terra Cave appears there
^ All Hoenn
Rain:
Hoenn - Route 119 (some days); Route 120 (always); Route 123 (some days); eastern Hoenn water routes (after Kyogre is awakened, before it is battled)SE; Routes 105, 125, 127, and 129 when Marine Cave appears there
Sinnoh - Route 212 (always); Route 213 (sometimes); Route 214 (south leg); Route 215 (always);
Johto; Lake of Rage (every day except Wednesday)
Unova : Routes 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 19, 20 in Unova (cycles based on current time); any routes containing roaming TornadusB/ThundurusW;Virbank City (sometimes) Driftveil City (sometimes) Icirrus City (Spring and Summer), Route 33
Sandstorm: Route 111 (Hoenn) , Route 228 (Sinnoh) , Route 4 (Unova)
Hail:
Sinnoh - Route 216; 217; Mt. Coronet peak; Mt. Silver peak
Unova - Route 6, Route 7, and near Dragonspiral Tower (winter only).
Shadow Sky: Nowhere :P
Fog:
Sinnoh - Route 210 (north leg); Lost TowerPt; Mt. Coronet basement; Victory Road (path to Route 224); Turnback Cave
Courtyard Colosseum (I have no idea where that is but its in Pokemon Colosseum)